It sounds to me like she is being treating for Psittacosis, in fact I'm sure of it. It's a bacterial infection that usually expresses itself with Respiratory symptoms and Conjunctivitis in the eyes, and the number one antibiotic used to treat it is Doxycycline, along with antibiotic eye drops to treat the Conjunctivitis...I have absolutely no idea why she was given the Bactrim though, it's a Sulfa-antibiotic that does not treat Psittacosis, but she may very well be allergic to Sulfa, and that may be what caused the seizure. It's very common for them to be allergic to Sulfa, and Sulfa drugs like Bactrim can also cause serious kidney issues as well, which can also lead to seizures.
My guess is that your Vet took Cultures and while waiting for the results, she put your bird on the Bactrim on a "just in case" basis, maybe they suspected something else was wrong that Bactrim would treat...However, upon getting the results of the Culture back, your vet diagnosed your bird definitively with Psittacosis, and then changed her antibiotic to the Doxycycline, as Bactrim doesn't treat it...Your bird should not be taking both the Bactrim and the Doxy, she absolutely needs the Doxy and the antibiotic eye drops, but not the Bactrim. I think there might have been some confusion about you replacing the Bactrim with the Doxy, and you accidentally started giving her both...Make sure that you clear this up with the vet at your appointment...
***The reason that your bird keeps "relapsing", and that is exactly what she is doing, is because the average length for treatment with oral Doxycycline for Psittacosis is 45-days. It used to be a 21-day round, but after many, many birds relapsing, they upped the recommended length of treatment with oral Doxy to 45-days. She needs to get her oral Doxy directly into her beak every single day for 45 days straight or the Psittacosis is not going to go away...Her outward symptoms are going away, but Psittacosis hides very well, and unless she's getting the correct dose of oral Doxy (based on her weight) every single day, directly into her mouth (not put into her water) for at least 45-days, then it's just going to keep coming back...
***The reason that she acquired a GI yeast/fungal infection is because she was taking two very strong antibiotics, and they killed-off all of the normal, healthy bacteria that is supposed to live throughout her GI Tract that kills-off the yeast/fungi and keeps it in-check...So i'm assuming that the Vet put her on also an Anti-Fungal med, that's the other med, though I don't know that for sure...She should be on both the Doxy and a prescription Anti-Fungal med, such as Nystatin or similar...In the meantime, I highly suggest that you start giving her an oral Probiotic supplement to replace the healthy bacteria in her gut, this will help to combat the Yeast infection, but she'll still need a prescription anti-fungal if she's not already on one, so be sure to talk to the vet about that too...You can buy her a Probiotic that you give her daily at any Petco. They sell both Benebac, which comes in a powder you put on her seeds once a day, and then also a paste that you have to give her directly into her mouth, as well as a bottle of Qwiko Avian Probiotic powder, which comes with a pre-measured scoop that you sprinkle on her food once daily. Either one is excellent, and I give all of my parrots the Qwiko Probiotic powder on their pellets once a day every day anyway, and it keeps their GI Tract healthy and does no harm, so it's a good daily supplement to give them regardless, but it will help your bird out tremendously right now.
I'm going to assume that your bird did have a seizure, and as already mentioned, the behavior that you described her having sounds exactly like what birds do just before they pass-away, so she's very lucky that she came back from that...The seizure may have been caused by the Bactrim because your bird is allegic to Sulfa or because it's causing her some kidney issues, or simply been caused because she is under such stress from being handled, or more likely because she was accidentally squeezed or compressed too hard while in the towel, which is easy to do, and she couldn't breath...However, it also could have been due to the Psittacosis as well, as she's been dealing with it for quite a while now, which is common because unless they get a long enough treatment with the antibiotic it will just keep coming back...OR, it could have been due to the secondary Fungal infection in her GI Tract due to the antibiotics, OR it could have been due to her being give two very strong antibiotics at the same time for so long...You'll never know why, just be glad that she made it through it...
****The main thing that you need to do now is to write down specific questions that you need to ask the vet and take the list with you, because you need to get her medication schedule worked-out immediately. She doesn't need to be on the Bactrim AND the Doxy IF her diagnosis is Psittacosis, so you need to make sure that you directly ask what her specific diagnosis actually is, and if it is Psittacosis...If the vet tells you that she was diagnosed with Psittacosis, then ask her how long she plans to keep her on the oral Doxy along with the Doxy injections (which are a good idea, as long as she gets an anti-fungal med as well), because if she keeps relapsing it is either because she has not been taking the Doxy every day for a long enough time (I'd ask the vet if they are aware that the new protocol for Psittacosis calls for a 45-day round of oral Doxy), OR because she needs to add a second antibiotic to take along with the Doxy, but not Bactrim...
Usually if a bird has Psittacosis and they do a 45-day round of daily, direct-oral Doxycycline and the Psittacosis comes back, they then add a second antibiotic and have the bird take another 21-day round of both the Doxy and the other antibiotic, which is usually either Tetracycline or Azithromycin. If your vet is using the Bactrim as the secondary antibiotic, I would request that she change the secondary antibiotic to Azithromycin to take along with another round of Doxy, because it's quite possible that your bird is allergic to Sulfa and that's what caused the seizure...
Also be sure to ask the vet about your bird getting an oral Anti-Fungal med, such as Nystatin, for the secondary Fungal infection, as well as asking them about starting her on a daily Probiotic supplement such as Benebac...
Psittacosis is not usually fatal in birds, but it is very difficult to get rid of completely because of how well it hides. So even if your bird finishes the Doxy and a blood test shows no bacteria or antibodies to the bacteria, suddenly in a day or two it can come right back. That's why it's important that she take the Doxy for a long enough time, AND that it is given to her directly into her mouth/beak and not put in her water...And if it's not working by itself, then adding Azithromycin is a very good idea, OR switching and trying Tetracycline instead of the Doxycycline, however Doxy does usually work when taken for 45-days straight...And the antibiotic eye drops that she was give, the Neo-Poly Dex eyedrops, they should get rid of the conjunctivitis in her eyes pretty quickly...does she still have any seeping from her eyes? If she does, be sure to get another bottle of the antibiotic drops...